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AtNUDT11 mediated dpCoA-RNA-seq defines epitranscriptomicdpCoA capped RNA [RNA-Seq]

ABSTRACT: Despite the parallel early discovery of dpCoA and NAD caps, dpCoA-RNA remains poorly characterized, largely due to the lack of selective decapping enzymes and reliable detection strategies. Evidence for its existence was limited to early bacterial studies，there is an urgent need for new and reliable technologies to quantify, identify, and investigate the molecular functions of the dpCoA cap.To map dpCoA-RNAs transcriptome-wide, we established dpCoA-RNA-seq, a sequencing method based on dpCoA decapping enzyme specificity, which revealed dpCoA-RNA features in Arabidopsis.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE302461 | GEO | 2026/01/26

REPOSITORIES: GEO

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AtNUDT11 mediated dpCoA-RNA-seq defines epitranscriptomicdpCoA capped RNA [dpCoA_seq]

Project description:Despite the parallel early discovery of dpCoA and NAD caps, dpCoA-RNA remains poorly characterized, largely due to the lack of selective decapping enzymes and reliable detection strategies. Evidence for its existence was limited to early bacterial studies，there is an urgent need for new and reliable technologies to quantify, identify, and investigate the molecular functions of the dpCoA cap.To map dpCoA-RNAs transcriptome-wide, we established dpCoA-RNA-seq, a sequencing method based on dpCoA decapping enzyme specificity, which revealed dpCoA-RNA features in Arabidopsis.

2026-01-26 | GSE302462 | GEO

Presence of NAD+-capped RNA in human cells: function and removal by the DXO deNADing Protein

Project description:Eukaryotic mRNAs generally possess an N7 methyl guanosine cap at their 5? end to promote their translation and stability. Here we demonstrate mammalian mRNAs can carry a 5'-end nicotinamide adenine dinucleotide (NAD+) cap. We further demonstrate fungal and mammalian noncanonical DXO family of decapping enzymes can efficiently remove NAD+ caps from mRNAs in vitro and cocrystal structures of DXO with 3´ phosphate NAD+ illuminates the molecular mechanism for the “deNADing” reaction. An NAD+ cap promotes mRNA decay in wild type mammalian cells and confers mRNA stability in the absence of DXO. Importantly, mammalian cells possess a capping mechanism that NAD+ caps a subset of intronic small nucleolar RNAs that are selectively enriched in DXO deficient cells. Our data establish NAD+ as a bona fide mammalian RNA cap and identifies the DXO proteins as potent deNADing enzymes that modulate the levels of NAD+-capped RNAs in cells.

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Decapping enzyme NUDT12 partners with BLMH for cytoplasmic surveillance of NAD-capped RNAs

Project description:RNA polymerase II transcripts receive a protective 5ʹ m7G cap early during transcription. An alternative cap can be acquired when RNA pol II initiation uses the redox cofactor nicotinamide adenine dinucleotide (NAD) to generate NAD-capped RNAs. The biology of mammalian NAD-RNAs, including its turnover and physiological roles are not completely understood. Here we identify NUDT12 as a cytosolic decapping enzyme for NAD-RNAs. Structural, biochemical and functional studies reveal how homodimerization modulates specificity of NUDT12 for NAD-RNAs as substrate. NUDT12 is localized within a few discrete cytoplasmic granules that are distinct from P-bodies. We identity Bleomycin hydrolase (BLMH) as a factor that associates with NUDT12 in a large ~600 kDa dodecamer complex, and we demonstrate that BLMH is required for correct localization of NUDT12 into these granules. This complex is functional in human cell cultures, as artificial tethering of BLMH to a reporter mRNA results in downregulation of reporter expression, similar to that seen with tethering of NUDT12. Analysis of mouse liver transcriptome from the Nudt12 knockout mouse reveals that a select set of RNAs are regulated, including a significant upregulation of circadian clock transcripts. Given that NAD biosynthesis is under circadian control, our study points to a physiological role for the cytosolic surveillance of NAD-RNAs.

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HIV-1 infection affects NAD capping of host cell snRNA and snoRNA

Project description:NAD besides its key role in cellular metabolism can serve as an alternative 5’ cap at several short non-coding RNAs. However, the function of the NAD cap remains elusive. Here, we investigate NAD capping of RNAs upon HIV-1 infection, which is associated with intracellular pellagra – depletion of NAD/NADH cellular pool. We applied NAD captureSeq on HIV-1 infected/noninfected cells and we revealed that four snRNAs (U1, U4ATAC, U5E and U7) and four snoRNAs (snord3G, snord102, snorA50A and snord3B) lost NAD cap upon HIV-1 infection. Interestingly, U1 snRNA was previously shown to be essential for HIV-1 replication. We provide evidence that the NAD cap reduces the stability of the U1 - HIV-1 pre-mRNA duplex. The importance of NAD RNA cap in HIV-1 infection was further supported by NAD decapping enzyme DXO overexpression, which led to increase in HIV-1 infectivity. This is the first example of NAD cap function in mammalian cells and suggests a general role of non-canonical RNA caps in antiviral innate immunity response.

2024-05-16 | GSE191019 | GEO

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SPAAC-NAD-seq, a sensitive and accurate method to profile NAD+-capped transcripts

Project description:We developed a Copper-free, strain-promoted azide-alkyne cycloaddition reaction (SPAAC) to capture NAD-RNAs without RNA degradation. We examined the specificity of CuAAC and SPAAC reactions towards NAD+ vs. m7G, and found that both prefer NAD+ but also act on m7G. We show that m7G-capped RNA can be immuno-depleted, allowing for the specific identification of NAD-RNA via the SPAAC reaction and sequencing, which we name SPAAC-NAD-seq. Subjecting Arabidopsis RNA to both the original NAD captureSeq and SPAAC-NAD-seq, we found that more NAD+-capped RNA was identified by the latter, particularly those with low abundance. This led to the discovery of new gene ontology terms such as starch biosynthsis, intracellular protein transport and response to cadmium stress associated with genes that produce NAD-RNA. Furthermore, reads were uniformly distributed along gene bodies, which suggested that SPAAC-NAD-seq retained full-length sequence information. SPAAC-NAD-seq enables specific and efficient discovery of NAD-RNA in prokaryotes, and when combined with m7G-RNA depletion, in eukaryotes.

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Decapping enzyme NUDT12 partners with BLMH for cytoplasmic surveillance of NAD-capped RNAs

Project description:Decapping enzyme NUDT12 partners with BLMH for cytoplasmic surveillance of NAD-capped RNAs

| PRJNA574161 | ENA